src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  24 import jalview.bin.Cache;
  25 import jalview.gui.Help.HelpId;
  26 import jalview.gui.StructureViewer.ViewerType;
  27 import jalview.io.BackupFiles;
  28 import jalview.io.FileFormatI;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.io.JalviewFileView;
  31 import jalview.jbgui.GPreferences;
  32 import jalview.jbgui.GSequenceLink;
  33 import jalview.schemes.ColourSchemeI;
  34 import jalview.schemes.ColourSchemes;
  35 import jalview.schemes.ResidueColourScheme;
  36 import jalview.urls.UrlLinkTableModel;
  37 import jalview.urls.api.UrlProviderFactoryI;
  38 import jalview.urls.api.UrlProviderI;
  39 import jalview.urls.desktop.DesktopUrlProviderFactory;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.util.UrlConstants;
  43 import jalview.ws.sifts.SiftsSettings;
  44
  45 import java.awt.BorderLayout;
  46 import java.awt.Color;
  47 import java.awt.Component;
  48 import java.awt.Dimension;
  49 import java.awt.Font;
  50 import java.awt.event.ActionEvent;
  51 import java.awt.event.ActionListener;
  52 import java.awt.event.MouseEvent;
  53 import java.io.File;
  54 import java.util.ArrayList;
  55 import java.util.List;
  56
  57 import javax.help.HelpSetException;
  58 import javax.swing.JColorChooser;
  59 import javax.swing.JFileChooser;
  60 import javax.swing.JInternalFrame;
  61 import javax.swing.JPanel;
  62 import javax.swing.ListSelectionModel;
  63 import javax.swing.RowFilter;
  64 import javax.swing.RowSorter;
  65 import javax.swing.SortOrder;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.ListSelectionEvent;
  69 import javax.swing.event.ListSelectionListener;
  70 import javax.swing.table.TableCellRenderer;
  71 import javax.swing.table.TableColumn;
  72 import javax.swing.table.TableModel;
  73 import javax.swing.table.TableRowSorter;
  74
  75 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  76
  77 /**
  78  * DOCUMENT ME!
  79  *
  80  * @author $author$
  81  * @version $Revision$
  82  */
  83 public class Preferences extends GPreferences
  84 {
  85   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  86
  87   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  88
  89   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  90
  91   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  92
  93   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  94
  95   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  96
  97   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  98
  99   public static final String USE_RNAVIEW = "USE_RNAVIEW";
 100
 101   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
 102
 103   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 104
 105   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 106
 107   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 108
 109   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 110
 111   public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
 112
 113   public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
 114
 115   public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
 116
 117   public static final String GAP_COLOUR = "GAP_COLOUR";
 118
 119   public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
 120
 121   private static final int MIN_FONT_SIZE = 1;
 122
 123   private static final int MAX_FONT_SIZE = 30;
 124
 125   /**
 126    * Holds name and link separated with | character. Sequence ID must be
 127    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
 128    */
 129   public static UrlProviderI sequenceUrlLinks;
 130
 131   public static UrlLinkTableModel dataModel;
 132
 133   /**
 134    * Holds name and link separated with | character. Sequence IDS and Sequences
 135    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 136    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 137    * for first and second token specified after a pipe character at end |,|.
 138    * (TODO: proper escape for using | to separate ids or sequences
 139    */
 140
 141   public static List<String> groupURLLinks;
 142   static
 143   {
 144     // get links selected to be in the menu (SEQUENCE_LINKS)
 145     // and links entered by the user but not selected (STORED_LINKS)
 146     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
 147     String notInMenuString = Cache.getDefault("STORED_LINKS", "");
 148     String defaultUrl = Cache.getDefault("DEFAULT_URL",
 149             UrlConstants.DEFAULT_LABEL);
 150
 151     // if both links lists are empty, add the DEFAULT_URL link
 152     // otherwise we assume the default link is in one of the lists
 153     if (inMenuString.isEmpty() && notInMenuString.isEmpty())
 154     {
 155       inMenuString = UrlConstants.DEFAULT_STRING;
 156     }
 157     UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
 158             inMenuString, notInMenuString);
 159     sequenceUrlLinks = factory.createUrlProvider();
 160     dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 161
 162     /**
 163      * TODO: reformulate groupURL encoding so two or more can be stored in the
 164      * .properties file as '|' separated strings
 165      */
 166
 167     groupURLLinks = new ArrayList<>();
 168   }
 169
 170   JInternalFrame frame;
 171
 172   private WsPreferences wsPrefs;
 173
 174   private OptionsParam promptEachTimeOpt = new OptionsParam(
 175           MessageManager.getString("label.prompt_each_time"),
 176           "Prompt each time");
 177
 178   private OptionsParam lineArtOpt = new OptionsParam(
 179           MessageManager.getString("label.lineart"), "Lineart");
 180
 181   private OptionsParam textOpt = new OptionsParam(
 182           MessageManager.getString("action.text"), "Text");
 183
 184   /**
 185    * Creates a new Preferences object.
 186    */
 187   public Preferences()
 188   {
 189     super();
 190     frame = new JInternalFrame();
 191     frame.setContentPane(this);
 192     wsPrefs = new WsPreferences();
 193     wsTab.add(wsPrefs, BorderLayout.CENTER);
 194     int width = 500, height = 450;
 195     new jalview.util.Platform();
 196     if (Platform.isAMac())
 197     {
 198       width = 570;
 199       height = 480;
 200     }
 201
 202     Desktop.addInternalFrame(frame,
 203             MessageManager.getString("label.preferences"), width, height);
 204     frame.setMinimumSize(new Dimension(width, height));
 205
 206     /*
 207      * Set Visual tab defaults
 208      */
 209     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 210     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 211     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 212     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 213
 214     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 215     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 216     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 217     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 218     showUnconserved
 219             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 220     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
 221     showGroupConsensus
 222             .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
 223     showGroupConservation.setSelected(
 224             Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
 225     showConsensHistogram.setSelected(
 226             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
 227     showConsensLogo
 228             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
 229     showNpTooltip
 230             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
 231     showDbRefTooltip
 232             .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 233
 234     String[] fonts = java.awt.GraphicsEnvironment
 235             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 236     for (int i = 0; i < fonts.length; i++)
 237     {
 238       fontNameCB.addItem(fonts[i]);
 239     }
 240
 241     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 242     {
 243       fontSizeCB.addItem(i + "");
 244     }
 245
 246     fontStyleCB.addItem("plain");
 247     fontStyleCB.addItem("bold");
 248     fontStyleCB.addItem("italic");
 249
 250     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 251     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 252     fontStyleCB.setSelectedItem(
 253             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 254
 255     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 256     scaleProteinToCdna
 257             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 258
 259     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 260
 261     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 262
 263     gapSymbolCB.addItem("-");
 264     gapSymbolCB.addItem(".");
 265
 266     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 267
 268     sortby.addItem("No sort");
 269     sortby.addItem("Id");
 270     sortby.addItem("Pairwise Identity");
 271     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 272
 273     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 274     sortAnnBy
 275             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 276     sortAnnBy
 277             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 278     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 279             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 280                     SequenceAnnotationOrder.NONE.name()));
 281     sortAnnBy.setSelectedItem(savedSort.toString());
 282
 283     sortAutocalc.addItem("Autocalculated first");
 284     sortAutocalc.addItem("Autocalculated last");
 285     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 286     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 287             : sortAutocalc.getItemAt(1));
 288     startupCheckbox
 289             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 290     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 291             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 292                     + "/examples/exampleFile_2_3.jar"));
 293
 294     /*
 295      * Set Colours tab defaults
 296      */
 297     protColour.addItem(ResidueColourScheme.NONE);
 298     nucColour.addItem(ResidueColourScheme.NONE);
 299     for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
 300     {
 301       String name = cs.getSchemeName();
 302       protColour.addItem(name);
 303       nucColour.addItem(name);
 304     }
 305     String oldProp = Cache.getDefault(DEFAULT_COLOUR,
 306             ResidueColourScheme.NONE);
 307     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 308     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 309     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 310     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 311     minColour.setBackground(
 312             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 313     maxColour.setBackground(
 314             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 315
 316     /*
 317      * Set overview panel defaults
 318      */
 319     gapColour.setBackground(
 320             Cache.getDefaultColour(GAP_COLOUR,
 321                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
 322     hiddenColour.setBackground(
 323             Cache.getDefaultColour(HIDDEN_COLOUR,
 324                     jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
 325     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
 326     gapLabel.setEnabled(!useLegacyGap.isSelected());
 327     gapColour.setEnabled(!useLegacyGap.isSelected());
 328     showHiddenAtStart
 329             .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
 330
 331     /*
 332      * Set Structure tab defaults.
 333      */
 334     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 335     structFromPdb.setSelected(structSelected);
 336     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 337     useRnaView.setEnabled(structSelected);
 338     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 339     addSecondaryStructure.setEnabled(structSelected);
 340     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 341     addTempFactor.setEnabled(structSelected);
 342     structViewer.setSelectedItem(
 343             Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
 344     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 345     chimeraPath.addActionListener(new ActionListener()
 346     {
 347       @Override
 348       public void actionPerformed(ActionEvent e)
 349       {
 350         validateChimeraPath();
 351       }
 352     });
 353
 354     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 355     {
 356       siftsMapping.setSelected(true);
 357     }
 358     else
 359     {
 360       nwMapping.setSelected(true);
 361     }
 362
 363     SiftsSettings
 364             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 365
 366     /*
 367      * Set Connections tab defaults
 368      */
 369
 370     // set up sorting
 371     linkUrlTable.setModel(dataModel);
 372     final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
 373             linkUrlTable.getModel());
 374     linkUrlTable.setRowSorter(sorter);
 375     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 376
 377     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
 378     sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
 379             SortOrder.DESCENDING));
 380     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
 381             SortOrder.DESCENDING));
 382     sortKeys.add(
 383             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 384
 385     sorter.setSortKeys(sortKeys);
 386     sorter.sort();
 387
 388     // set up filtering
 389     ActionListener onReset;
 390     onReset = new ActionListener()
 391     {
 392       @Override
 393       public void actionPerformed(ActionEvent e)
 394       {
 395         filterTB.setText("");
 396         sorter.setRowFilter(RowFilter.regexFilter(""));
 397       }
 398
 399     };
 400     doReset.addActionListener(onReset);
 401
 402     // filter to display only custom urls
 403     final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
 404     {
 405       @Override
 406       public boolean include(
 407               Entry<? extends TableModel, ? extends Object> entry)
 408       {
 409         return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
 410       }
 411     };
 412
 413     final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
 414             linkUrlTable.getModel());
 415     customSorter.setRowFilter(customUrlFilter);
 416
 417     ActionListener onCustomOnly;
 418     onCustomOnly = new ActionListener()
 419     {
 420       @Override
 421       public void actionPerformed(ActionEvent e)
 422       {
 423         filterTB.setText("");
 424         sorter.setRowFilter(customUrlFilter);
 425       }
 426     };
 427     userOnly.addActionListener(onCustomOnly);
 428
 429     filterTB.getDocument().addDocumentListener(new DocumentListener()
 430     {
 431       String caseInsensitiveFlag = "(?i)";
 432
 433       @Override
 434       public void changedUpdate(DocumentEvent e)
 435       {
 436         sorter.setRowFilter(RowFilter
 437                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 438       }
 439
 440       @Override
 441       public void removeUpdate(DocumentEvent e)
 442       {
 443         sorter.setRowFilter(RowFilter
 444                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 445       }
 446
 447       @Override
 448       public void insertUpdate(DocumentEvent e)
 449       {
 450         sorter.setRowFilter(RowFilter
 451                 .regexFilter(caseInsensitiveFlag + filterTB.getText()));
 452       }
 453     });
 454
 455     // set up list selection functionality
 456     linkUrlTable.getSelectionModel()
 457             .addListSelectionListener(new UrlListSelectionHandler());
 458
 459     // set up radio buttons
 460     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 461             .getPrimaryColumn();
 462     String onClickName = linkUrlTable.getColumnName(onClickCol);
 463     linkUrlTable.getColumn(onClickName)
 464             .setCellRenderer(new RadioButtonRenderer());
 465     linkUrlTable.getColumn(onClickName)
 466             .setCellEditor(new RadioButtonEditor());
 467
 468     // get boolean columns and resize those to min possible
 469     for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
 470     {
 471       if (linkUrlTable.getModel().getColumnClass(column)
 472               .equals(Boolean.class))
 473       {
 474         TableColumn tableColumn = linkUrlTable.getColumnModel()
 475                 .getColumn(column);
 476         int preferredWidth = tableColumn.getMinWidth();
 477
 478         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
 479                 column);
 480         Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
 481         int cwidth = c.getPreferredSize().width
 482                 + linkUrlTable.getIntercellSpacing().width;
 483         preferredWidth = Math.max(preferredWidth, cwidth);
 484
 485         tableColumn.setPreferredWidth(preferredWidth);
 486       }
 487     }
 488
 489     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 490     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
 491     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 492     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 493
 494     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 495
 496     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 497     // note antisense here: default is true
 498     questionnaire
 499             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 500     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 501
 502     /*
 503      * Set Output tab defaults
 504      */
 505     epsRendering.addItem(promptEachTimeOpt);
 506     epsRendering.addItem(lineArtOpt);
 507     epsRendering.addItem(textOpt);
 508     String defaultEPS = Cache.getDefault("EPS_RENDERING",
 509             "Prompt each time");
 510     if (defaultEPS.equalsIgnoreCase("Text"))
 511     {
 512       epsRendering.setSelectedItem(textOpt);
 513     }
 514     else if (defaultEPS.equalsIgnoreCase("Lineart"))
 515     {
 516       epsRendering.setSelectedItem(lineArtOpt);
 517     }
 518     else
 519     {
 520       epsRendering.setSelectedItem(promptEachTimeOpt);
 521     }
 522     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 523     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 524     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 525     Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
 526     userIdWidth.setText(wi == null ? "" : wi.toString());
 527     // TODO: refactor to use common enum via FormatAdapter and allow extension
 528     // for new flat file formats
 529     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 530     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 531     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 532     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 533     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 534     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 535     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 536     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 537     embbedBioJSON
 538             .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 539
 540     /*
 541      * Set Editing tab defaults
 542      */
 543     autoCalculateConsCheck
 544             .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
 545     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 546     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 547
 548     annotations_actionPerformed(null); // update the display of the annotation
 549                                        // settings
 550   }
 551
 552   /**
 553    * Save user selections on the Preferences tabs to the Cache and write out to
 554    * file.
 555    *
 556    * @param e
 557    */
 558   @Override
 559   public void ok_actionPerformed(ActionEvent e)
 560   {
 561     if (!validateSettings())
 562     {
 563       return;
 564     }
 565
 566     /*
 567      * Save Visual settings
 568      */
 569     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 570             Boolean.toString(seqLimit.isSelected()));
 571     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 572             Boolean.toString(rightAlign.isSelected()));
 573     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 574             Boolean.toString(fullScreen.isSelected()));
 575     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 576             Boolean.toString(openoverv.isSelected()));
 577     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 578             Boolean.toString(annotations.isSelected()));
 579     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 580             Boolean.toString(conservation.isSelected()));
 581     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 582             Boolean.toString(quality.isSelected()));
 583     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 584             Boolean.toString(identity.isSelected()));
 585
 586     Cache.applicationProperties.setProperty("GAP_SYMBOL",
 587             gapSymbolCB.getSelectedItem().toString());
 588
 589     Cache.applicationProperties.setProperty("FONT_NAME",
 590             fontNameCB.getSelectedItem().toString());
 591     Cache.applicationProperties.setProperty("FONT_STYLE",
 592             fontStyleCB.getSelectedItem().toString());
 593     Cache.applicationProperties.setProperty("FONT_SIZE",
 594             fontSizeCB.getSelectedItem().toString());
 595
 596     Cache.applicationProperties.setProperty("ID_ITALICS",
 597             Boolean.toString(idItalics.isSelected()));
 598     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 599             Boolean.toString(showUnconserved.isSelected()));
 600     Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
 601             Boolean.toString(showOccupancy.isSelected()));
 602     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 603             Boolean.toString(showGroupConsensus.isSelected()));
 604     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 605             Boolean.toString(showGroupConservation.isSelected()));
 606     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 607             Boolean.toString(showConsensHistogram.isSelected()));
 608     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 609             Boolean.toString(showConsensLogo.isSelected()));
 610     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 611             Boolean.toString(smoothFont.isSelected()));
 612     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 613             Boolean.toString(scaleProteinToCdna.isSelected()));
 614     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 615             Boolean.toString(showNpTooltip.isSelected()));
 616     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 617             Boolean.toString(showDbRefTooltip.isSelected()));
 618
 619     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 620             Boolean.toString(wrap.isSelected()));
 621
 622     Cache.applicationProperties.setProperty("STARTUP_FILE",
 623             startupFileTextfield.getText());
 624     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 625             Boolean.toString(startupCheckbox.isSelected()));
 626
 627     Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
 628             sortby.getSelectedItem().toString());
 629
 630     // convert description of sort order to enum name for save
 631     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 632             .forDescription(sortAnnBy.getSelectedItem().toString());
 633     if (annSortOrder != null)
 634     {
 635       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 636               annSortOrder.name());
 637     }
 638
 639     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 640     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 641             Boolean.valueOf(showAutocalcFirst).toString());
 642
 643     /*
 644      * Save Colours settings
 645      */
 646     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
 647             protColour.getSelectedItem().toString());
 648     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
 649             nucColour.getSelectedItem().toString());
 650     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 651             minColour.getBackground());
 652     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 653             maxColour.getBackground());
 654
 655     /*
 656      * Save Overview settings
 657      */
 658     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
 659     Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
 660     Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
 661             Boolean.toString(useLegacyGap.isSelected()));
 662     Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
 663             Boolean.toString(showHiddenAtStart.isSelected()));
 664
 665     /*
 666      * Save Structure settings
 667      */
 668     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 669             Boolean.toString(addTempFactor.isSelected()));
 670     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 671             Boolean.toString(addSecondaryStructure.isSelected()));
 672     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 673             Boolean.toString(useRnaView.isSelected()));
 674     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 675             Boolean.toString(structFromPdb.isSelected()));
 676     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
 677             structViewer.getSelectedItem().toString());
 678     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 679     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 680             Boolean.toString(siftsMapping.isSelected()));
 681     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 682
 683     /*
 684      * Save Output settings
 685      */
 686     Cache.applicationProperties.setProperty("EPS_RENDERING",
 687             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
 688
 689     /*
 690      * Save Connections settings
 691      */
 692     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 693
 694     jalview.util.BrowserLauncher.resetBrowser();
 695
 696     // save user-defined and selected links
 697     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
 698     if (menuLinks.isEmpty())
 699     {
 700       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 701     }
 702     else
 703     {
 704       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 705               menuLinks.toString());
 706     }
 707
 708     String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
 709     if (nonMenuLinks.isEmpty())
 710     {
 711       Cache.applicationProperties.remove("STORED_LINKS");
 712     }
 713     else
 714     {
 715       Cache.applicationProperties.setProperty("STORED_LINKS",
 716               nonMenuLinks.toString());
 717     }
 718
 719     Cache.applicationProperties.setProperty("DEFAULT_URL",
 720             sequenceUrlLinks.getPrimaryUrlId());
 721
 722     Cache.applicationProperties.setProperty("USE_PROXY",
 723             Boolean.toString(useProxy.isSelected()));
 724
 725     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 726
 727     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 728
 729     if (useProxy.isSelected())
 730     {
 731       System.setProperty("http.proxyHost", proxyServerTB.getText());
 732       System.setProperty("http.proxyPort", proxyPortTB.getText());
 733     }
 734     else
 735     {
 736       System.setProperty("http.proxyHost", "");
 737       System.setProperty("http.proxyPort", "");
 738     }
 739     Cache.setProperty("VERSION_CHECK",
 740             Boolean.toString(versioncheck.isSelected()));
 741     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 742     {
 743       // default is false - we only set this if the user has actively agreed
 744       Cache.setProperty("USAGESTATS",
 745               Boolean.toString(usagestats.isSelected()));
 746     }
 747     if (!questionnaire.isSelected())
 748     {
 749       Cache.setProperty("NOQUESTIONNAIRES", "true");
 750     }
 751     else
 752     {
 753       // special - made easy to edit a property file to disable questionnaires
 754       // by just adding the given line
 755       Cache.removeProperty("NOQUESTIONNAIRES");
 756     }
 757
 758     /*
 759      * Save Output settings
 760      */
 761     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 762             Boolean.toString(blcjv.isSelected()));
 763     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 764             Boolean.toString(clustaljv.isSelected()));
 765     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 766             Boolean.toString(fastajv.isSelected()));
 767     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 768             Boolean.toString(msfjv.isSelected()));
 769     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 770             Boolean.toString(pfamjv.isSelected()));
 771     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 772             Boolean.toString(pileupjv.isSelected()));
 773     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 774             Boolean.toString(pirjv.isSelected()));
 775     Cache.applicationProperties.setProperty("PIR_MODELLER",
 776             Boolean.toString(modellerOutput.isSelected()));
 777     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 778             Boolean.toString(embbedBioJSON.isSelected()));
 779     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 780
 781     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 782             Boolean.toString(autoIdWidth.isSelected()));
 783     userIdWidth_actionPerformed();
 784     Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
 785             userIdWidth.getText());
 786
 787     /*
 788      * Save Editing settings
 789      */
 790     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 791             Boolean.toString(autoCalculateConsCheck.isSelected()));
 792     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 793             Boolean.toString(sortByTree.isSelected()));
 794     Cache.applicationProperties.setProperty("PAD_GAPS",
 795             Boolean.toString(padGaps.isSelected()));
 796
 797     wsPrefs.updateAndRefreshWsMenuConfig(false);
 798
 799     /*
 800      * Save Backups settings
 801      */
 802     Cache.applicationProperties.setProperty(BackupFiles.CONFIRM_DELETE_OLD,
 803             Boolean.toString(backupfilesConfirmDelete.isSelected()));
 804     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
 805             Boolean.toString(enableBackupFiles.isSelected()));
 806     Cache.applicationProperties.setProperty(BackupFiles.NO_MAX,
 807             Boolean.toString(backupfilesKeepAll.isSelected()));
 808     Cache.applicationProperties.setProperty(BackupFiles.REVERSE_ORDER,
 809             Boolean.toString(suffixReverse.isSelected()));
 810     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX,
 811             suffixTemplate.getText());
 812     Cache.applicationProperties.setProperty(BackupFiles.ROLL_MAX,
 813             Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
 814     Cache.applicationProperties.setProperty(BackupFiles.SUFFIX_DIGITS,
 815             Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
 816
 817     Cache.saveProperties();
 818     Desktop.instance.doConfigureStructurePrefs();
 819     try
 820     {
 821       frame.setClosed(true);
 822     } catch (Exception ex)
 823     {
 824     }
 825   }
 826
 827   /**
 828    * Do any necessary validation before saving settings. Return focus to the
 829    * first tab which fails validation.
 830    *
 831    * @return
 832    */
 833   private boolean validateSettings()
 834   {
 835     if (!validateStructure())
 836     {
 837       structureTab.requestFocusInWindow();
 838       return false;
 839     }
 840     return true;
 841   }
 842
 843   @Override
 844   protected boolean validateStructure()
 845   {
 846     return validateChimeraPath();
 847
 848   }
 849
 850   /**
 851    * DOCUMENT ME!
 852    */
 853   @Override
 854   public void startupFileTextfield_mouseClicked()
 855   {
 856     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
 857     JalviewFileChooser chooser = JalviewFileChooser
 858             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 859     chooser.setFileView(new JalviewFileView());
 860     chooser.setDialogTitle(
 861             MessageManager.getString("label.select_startup_file"));
 862
 863     int value = chooser.showOpenDialog(this);
 864
 865     if (value == JalviewFileChooser.APPROVE_OPTION)
 866     {
 867       FileFormatI format = chooser.getSelectedFormat();
 868       if (format != null)
 869       {
 870         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
 871                 format.getName());
 872       }
 873       startupFileTextfield
 874               .setText(chooser.getSelectedFile().getAbsolutePath());
 875     }
 876   }
 877
 878   /**
 879    * DOCUMENT ME!
 880    *
 881    * @param e
 882    *          DOCUMENT ME!
 883    */
 884   @Override
 885   public void cancel_actionPerformed(ActionEvent e)
 886   {
 887     try
 888     {
 889       wsPrefs.updateWsMenuConfig(true);
 890       wsPrefs.refreshWs_actionPerformed(e);
 891       frame.setClosed(true);
 892     } catch (Exception ex)
 893     {
 894     }
 895   }
 896
 897   /**
 898    * DOCUMENT ME!
 899    *
 900    * @param e
 901    *          DOCUMENT ME!
 902    */
 903   @Override
 904   public void annotations_actionPerformed(ActionEvent e)
 905   {
 906     conservation.setEnabled(annotations.isSelected());
 907     quality.setEnabled(annotations.isSelected());
 908     identity.setEnabled(annotations.isSelected());
 909     showOccupancy.setEnabled(annotations.isSelected());
 910     showGroupConsensus.setEnabled(annotations.isSelected());
 911     showGroupConservation.setEnabled(annotations.isSelected());
 912     showConsensHistogram.setEnabled(annotations.isSelected()
 913             && (identity.isSelected() || showGroupConsensus.isSelected()));
 914     showConsensLogo.setEnabled(annotations.isSelected()
 915             && (identity.isSelected() || showGroupConsensus.isSelected()));
 916   }
 917
 918   @Override
 919   public void newLink_actionPerformed(ActionEvent e)
 920   {
 921     GSequenceLink link = new GSequenceLink();
 922     boolean valid = false;
 923     while (!valid)
 924     {
 925       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 926               MessageManager.getString("label.new_sequence_url_link"),
 927               JvOptionPane.OK_CANCEL_OPTION, -1,
 928               null) == JvOptionPane.OK_OPTION)
 929       {
 930         if (link.checkValid())
 931         {
 932           if (((UrlLinkTableModel) linkUrlTable.getModel())
 933                   .isUniqueName(link.getName()))
 934           {
 935             ((UrlLinkTableModel) linkUrlTable.getModel())
 936                     .insertRow(link.getName(), link.getURL());
 937             valid = true;
 938           }
 939           else
 940           {
 941             link.notifyDuplicate();
 942             continue;
 943           }
 944         }
 945       }
 946       else
 947       {
 948         break;
 949       }
 950     }
 951   }
 952
 953   @Override
 954   public void editLink_actionPerformed(ActionEvent e)
 955   {
 956     GSequenceLink link = new GSequenceLink();
 957
 958     int index = linkUrlTable.getSelectedRow();
 959     if (index == -1)
 960     {
 961       // button no longer enabled if row is not selected
 962       Cache.log.debug("Edit with no row selected in linkUrlTable");
 963       return;
 964     }
 965
 966     int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 967             .getNameColumn();
 968     int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
 969             .getUrlColumn();
 970     String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
 971     link.setName(oldName);
 972     link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 973
 974     boolean valid = false;
 975     while (!valid)
 976     {
 977       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 978               MessageManager.getString("label.edit_sequence_url_link"),
 979               JvOptionPane.OK_CANCEL_OPTION, -1,
 980               null) == JvOptionPane.OK_OPTION)
 981       {
 982         if (link.checkValid())
 983         {
 984           if ((oldName.equals(link.getName()))
 985                   || (((UrlLinkTableModel) linkUrlTable.getModel())
 986                           .isUniqueName(link.getName())))
 987           {
 988             linkUrlTable.setValueAt(link.getName(), index, nameCol);
 989             linkUrlTable.setValueAt(link.getURL(), index, urlCol);
 990             valid = true;
 991           }
 992           else
 993           {
 994             link.notifyDuplicate();
 995             continue;
 996           }
 997         }
 998       }
 999       else
1000       {
1001         break;
1002       }
1003     }
1004   }
1005
1006   @Override
1007   public void deleteLink_actionPerformed(ActionEvent e)
1008   {
1009     int index = linkUrlTable.getSelectedRow();
1010     int modelIndex = -1;
1011     if (index == -1)
1012     {
1013       // button no longer enabled if row is not selected
1014       Cache.log.debug("Delete with no row selected in linkUrlTable");
1015       return;
1016     }
1017     else
1018     {
1019       modelIndex = linkUrlTable.convertRowIndexToModel(index);
1020     }
1021
1022     // make sure we use the model index to delete, and not the table index
1023     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
1024   }
1025
1026   @Override
1027   public void defaultBrowser_mouseClicked(MouseEvent e)
1028   {
1029     JFileChooser chooser = new JFileChooser(".");
1030     chooser.setDialogTitle(
1031             MessageManager.getString("label.select_default_browser"));
1032
1033     int value = chooser.showOpenDialog(this);
1034
1035     if (value == JFileChooser.APPROVE_OPTION)
1036     {
1037       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
1038     }
1039
1040   }
1041
1042   /*
1043    * (non-Javadoc)
1044    *
1045    * @see
1046    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
1047    * .ActionEvent)
1048    */
1049   @Override
1050   protected void showunconserved_actionPerformed(ActionEvent e)
1051   {
1052     // TODO Auto-generated method stub
1053     super.showunconserved_actionPerformed(e);
1054   }
1055
1056   public static List<String> getGroupURLLinks()
1057   {
1058     return groupURLLinks;
1059   }
1060
1061   @Override
1062   public void minColour_actionPerformed(JPanel panel)
1063   {
1064     Color col = JColorChooser.showDialog(this,
1065             MessageManager.getString("label.select_colour_minimum_value"),
1066             minColour.getBackground());
1067     if (col != null)
1068     {
1069       panel.setBackground(col);
1070     }
1071     panel.repaint();
1072   }
1073
1074   @Override
1075   public void maxColour_actionPerformed(JPanel panel)
1076   {
1077     Color col = JColorChooser.showDialog(this,
1078             MessageManager.getString("label.select_colour_maximum_value"),
1079             maxColour.getBackground());
1080     if (col != null)
1081     {
1082       panel.setBackground(col);
1083     }
1084     panel.repaint();
1085   }
1086
1087   @Override
1088   public void gapColour_actionPerformed(JPanel gap)
1089   {
1090     if (!useLegacyGap.isSelected())
1091     {
1092       Color col = JColorChooser.showDialog(this,
1093               MessageManager.getString("label.select_gap_colour"),
1094               gapColour.getBackground());
1095       if (col != null)
1096       {
1097         gap.setBackground(col);
1098       }
1099       gap.repaint();
1100     }
1101   }
1102
1103   @Override
1104   public void hiddenColour_actionPerformed(JPanel hidden)
1105   {
1106     Color col = JColorChooser.showDialog(this,
1107             MessageManager.getString("label.select_hidden_colour"),
1108             hiddenColour.getBackground());
1109     if (col != null)
1110     {
1111       hidden.setBackground(col);
1112     }
1113     hidden.repaint();
1114   }
1115
1116   @Override
1117   protected void useLegacyGaps_actionPerformed(ActionEvent e)
1118   {
1119     boolean enabled = useLegacyGap.isSelected();
1120     if (enabled)
1121     {
1122       gapColour.setBackground(
1123               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
1124     }
1125     else
1126     {
1127       gapColour.setBackground(
1128               jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
1129     }
1130     gapColour.setEnabled(!enabled);
1131     gapLabel.setEnabled(!enabled);
1132   }
1133
1134   @Override
1135   protected void resetOvDefaults_actionPerformed(ActionEvent e)
1136   {
1137     useLegacyGap.setSelected(false);
1138     useLegacyGaps_actionPerformed(null);
1139     showHiddenAtStart.setSelected(true);
1140     hiddenColour.setBackground(
1141             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
1142   }
1143
1144   @Override
1145   protected void userIdWidth_actionPerformed()
1146   {
1147     try
1148     {
1149       String val = userIdWidth.getText().trim();
1150       if (val.length() > 0)
1151       {
1152         Integer iw = Integer.parseInt(val);
1153         if (iw.intValue() < 12)
1154         {
1155           throw new NumberFormatException();
1156         }
1157         userIdWidth.setText(iw.toString());
1158       }
1159     } catch (NumberFormatException x)
1160     {
1161       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1162               MessageManager
1163                       .getString("warn.user_defined_width_requirements"),
1164               MessageManager.getString("label.invalid_id_column_width"),
1165               JvOptionPane.WARNING_MESSAGE);
1166       userIdWidth.setText("");
1167     }
1168   }
1169
1170   @Override
1171   protected void autoIdWidth_actionPerformed()
1172   {
1173     userIdWidth.setEnabled(!autoIdWidth.isSelected());
1174     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
1175   }
1176
1177   /**
1178    * Returns true if chimera path is to a valid executable, else show an error
1179    * dialog.
1180    */
1181   private boolean validateChimeraPath()
1182   {
1183     if (chimeraPath.getText().trim().length() > 0)
1184     {
1185       File f = new File(chimeraPath.getText());
1186       if (!f.canExecute())
1187       {
1188         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1189                 MessageManager.getString("label.invalid_chimera_path"),
1190                 MessageManager.getString("label.invalid_name"),
1191                 JvOptionPane.ERROR_MESSAGE);
1192         return false;
1193       }
1194     }
1195     return true;
1196   }
1197
1198   /**
1199    * If Chimera is selected, check it can be found on default or user-specified
1200    * path, if not show a warning/help dialog.
1201    */
1202   @Override
1203   protected void structureViewer_actionPerformed(String selectedItem)
1204   {
1205     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
1206     {
1207       return;
1208     }
1209     boolean found = false;
1210
1211     /*
1212      * Try user-specified and standard paths for Chimera executable.
1213      */
1214     List<String> paths = StructureManager.getChimeraPaths();
1215     paths.add(0, chimeraPath.getText());
1216     for (String path : paths)
1217     {
1218       if (new File(path.trim()).canExecute())
1219       {
1220         found = true;
1221         break;
1222       }
1223     }
1224     if (!found)
1225     {
1226       String[] options = { "OK", "Help" };
1227       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
1228               JvSwingUtils.wrapTooltip(true,
1229                       MessageManager.getString("label.chimera_missing")),
1230               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
1231               null, options, options[0]);
1232       if (showHelp == JvOptionPane.NO_OPTION)
1233       {
1234         try
1235         {
1236           Help.showHelpWindow(HelpId.StructureViewer);
1237         } catch (HelpSetException e)
1238         {
1239           e.printStackTrace();
1240         }
1241       }
1242     }
1243   }
1244
1245   public class OptionsParam
1246   {
1247     private String name;
1248
1249     private String code;
1250
1251     public OptionsParam(String name, String code)
1252     {
1253       this.name = name;
1254       this.code = code;
1255     }
1256
1257     public String getName()
1258     {
1259       return name;
1260     }
1261
1262     public void setName(String name)
1263     {
1264       this.name = name;
1265     }
1266
1267     public String getCode()
1268     {
1269       return code;
1270     }
1271
1272     public void setCode(String code)
1273     {
1274       this.code = code;
1275     }
1276
1277     @Override
1278     public String toString()
1279     {
1280       return name;
1281     }
1282
1283     @Override
1284     public boolean equals(Object that)
1285     {
1286       if (!(that instanceof OptionsParam))
1287       {
1288         return false;
1289       }
1290       return this.code.equalsIgnoreCase(((OptionsParam) that).code);
1291     }
1292
1293     @Override
1294     public int hashCode()
1295     {
1296       return name.hashCode() + code.hashCode();
1297     }
1298   }
1299
1300   private class UrlListSelectionHandler implements ListSelectionListener
1301   {
1302
1303     @Override
1304     public void valueChanged(ListSelectionEvent e)
1305     {
1306       ListSelectionModel lsm = (ListSelectionModel) e.getSource();
1307
1308       int index = lsm.getMinSelectionIndex();
1309       if (index == -1)
1310       {
1311         // no selection, so disable delete/edit buttons
1312         editLink.setEnabled(false);
1313         deleteLink.setEnabled(false);
1314         return;
1315       }
1316       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
1317
1318       // enable/disable edit and delete link buttons
1319       if (((UrlLinkTableModel) linkUrlTable.getModel())
1320               .isRowDeletable(modelIndex))
1321       {
1322         deleteLink.setEnabled(true);
1323       }
1324       else
1325       {
1326         deleteLink.setEnabled(false);
1327       }
1328
1329       if (((UrlLinkTableModel) linkUrlTable.getModel())
1330               .isRowEditable(modelIndex))
1331       {
1332         editLink.setEnabled(true);
1333       }
1334       else
1335       {
1336         editLink.setEnabled(false);
1337       }
1338     }
1339   }
1340 }